[Bioperl-l] looks like a Bio::SeqIO error

[Chris Fields]

Just curious, but why not use something like Bio::DB::Fasta?  It may  
be better suited for something like this.

chris


On May 15, 2009, at 8:17 AM, fungazid wrote:

> Hello,
>
> I hope this is the right address for bioperl programming issues.  
> Bioperl
> saves me a lot of time (not to re-invent the wheel), but there are  
> some
> extremely irritating problems (I would change the code myself if I  
> knew
> how).
>
> I am trying to read a file (~20MB) containing multiple fasta  
> sequences:
>> a
> AGTAGTGAGTGCGCTGA.........
>> b
> GCGCTGAAGTAGTGAGT.......
>> c
> AGTAGTGAGTGCGCTGA.........
>> d...........
>
> with the following lines:
>
> my $seqin = Bio::SeqIO->new('-format'=>'largefasta','-file'=>$file1);
>
> LOOP1: while ( my $seqobj1 = $seqin->next_seq())
>
> {
> ......
> my $seq=$seqobj1->subseq(1,$seqobj1->length);
> .......
> }
>
>
> This works right for the first ~30000 contig sequences but then the
> following message appears:
>
> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory
> /tmp/6eS92VzVjm: Too many links at /usr/share/perl5/Bio/Root/IO.pm  
> line 744
>
> What to do ??? (this is only one of some different Bioperl related  
> bugs that
> I'm experiencing)
>
>
>
>
> -- 
> View this message in context: http://www.nabble.com/looks-like-a-Bio%3A%3ASeqIO-error-tp23559474p23559474.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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